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Challenges and standards in integrating surveys of structural variation

Nature Genetics volume 39, pages S7–S15 (2007)Cite this article

Abstract

There has been an explosion of data describing newly recognized structural variants in the human genome. In the flurry of reporting, there has been no standard approach to collecting the data, assessing its quality or describing identified features. This risks becoming a rampant problem, in particular with respect to surveys of copy number variation and their application to disease studies. Here, we consider the challenges in characterizing and documenting genomic structural variants. From this, we derive recommendations for standards to be adopted, with the aim of ensuring the accurate presentation of this form of genetic variation to facilitate ongoing research.

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Figure 1: Lexicon of genomic variation.

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Acknowledgements

We thank Dr. Janet Buchanan for assistance in manuscript preparation and D. Pinto, C. Marshall, R. Redon, I. Ragoussis and A. Carson for sharing ideas and unpublished data. The work is supported by Genome Canada/Ontario Genomics Institute, The Centre for Applied Genomics, the Canadian Institutes of Health Research (CIHR), the McLaughlin Centre for Molecular Medicine, the Canadian Institute of Advanced Research and the Hospital for Sick Children Foundation. M.E.H. and N.P.C. are supported by the Wellcome Trust. L.F. is supported by CIHR and S.W.S. is an Investigator of CIHR and holds the GlaxoSmithKline/CIHR Pathfinder Chair in Genetics and Genomics at the Hospital for Sick Children and the University of Toronto.

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Authors and Affiliations

  1. Stephen W. Scherer and Lars Feuk are at The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, 14th Floor, Toronto Medical Discovery Tower, MaRS Discovery District, 101 College Street, Room 14-701, Ontario M5G 1L7, Canada.,

    Stephen W Scherer & Lars Feuk

  2. Stephen W. Scherer is in the Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M5G 1L7, Canada. steve@genet.sickkids.on.ca,

    Stephen W Scherer

  3. Charles Lee is in the Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.,

    Charles Lee

  4. Ewan Birney is at the European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,

    Ewan Birney

  5. Nigel P. Carter and Matthew E. Hurles are at the Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,

    Nigel P Carter & Matthew E Hurles

  6. David M. Altshuler is in the Program in Medical and Population Genetics, Broad Institute of Harvard University and the Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.,

    David M Altshuler

  7. Evan E. Eichler is in the Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, Washington 98195, USA.,

    Evan E Eichler

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Supplementary information

Supplementary Fig. 1

Complexities of assessing different classes of copy number variants (CNVs). (PDF 36 kb)

Supplementary Fig. 2

A hypothetical genomic region and the ability of different screening technology platforms to identify particular structural variants. (PDF 18 kb)

Supplementary Fig. 3

CNVs within regions of segmental duplication. (PDF 51 kb)

Supplementary Table 1

Comparison of CNVs detected with different platforms and analysis tools. (PDF 9 kb)

Supplementary Table 2

Summary of 12 published surveys (2004–2007) of structural variation content in human genomes. (PDF 89 kb)

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Scherer, S., Lee, C., Birney, E. et al. Challenges and standards in integrating surveys of structural variation. Nat Genet 39 (Suppl 7), S7–S15 (2007). https://doi.org/10.1038/ng2093

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